Change 1 : patch the help message to take into account option added and the new output format.
Change 2 : Change the used rules to define example and counter example taxon sets. By default all taxa are example taxa and no counterexample taxa are used. By using -r option (one or several time) you could restict example taxa to a subset of taxa In old version all taxa not in example set are in the counterexample set. Now restrict example set with -r option doesn't define the counter example set. You must use -i to define the conterexample set in a similar way or -r option for example taxa. git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@234 60f365c0-8329-0410-b2a4-ec073aeeaa1d
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